NM_001395229.1:c.90+1077T>C

Variant names:

• chr13-114180497-T-C
• rs6560936
• NM_001395229.1:c.90+1077T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001395229.1(CFAP97D2):​c.90+1077T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,974 control chromosomes in the GnomAD database, including 28,984 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.61 (28984 hom., cov: 32)
• Consequence: CFAP97D2 NM_001395229.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537
• Publications: 5 publications found

Genes affected

CFAP97D2 (HGNC:53789): (CFAP97 domain containing 2)

ENSG00000283347 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395229.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP97D2	NM_001395229.1	MANE Select	c.90+1077T>C		intron	N/A	NP_001382158.1
	CFAP97D2	NM_001437370.1		c.90+1077T>C		intron	N/A	NP_001424299.1
	CFAP97D2	NM_001395230.1		c.90+1077T>C		intron	N/A	NP_001382159.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CFAP97D2	ENST00000636692.2	TSL:5 MANE Select	c.90+1077T>C		intron	N/A	ENSP00000489989.1
	CFAP97D2	ENST00000646158.1		c.90+1077T>C		intron	N/A	ENSP00000496151.1
	CFAP97D2	ENST00000635901.2	TSL:5	c.90+1077T>C		intron	N/A	ENSP00000490372.1

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92290 AN: 151856 Hom.: 28943 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.648

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.602

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.608 AC: 92384 AN: 151974 Hom.: 28984 Cov.: 32 AF XY: 0.608 AC XY: 45186 AN XY: 74274

African (AFR) AF: 0.770 AC: 31928 AN: 41462

American (AMR) AF: 0.580 AC: 8861 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1791 AN: 3468

East Asian (EAS) AF: 0.749 AC: 3865 AN: 5160

South Asian (SAS) AF: 0.591 AC: 2845 AN: 4816

European-Finnish (FIN) AF: 0.540 AC: 5702 AN: 10550

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35359 AN: 67922

Other (OTH) AF: 0.602 AC: 1272 AN: 2112

Alfa AF: 0.585 Hom.: 5160

Bravo AF: 0.621

Asia WGS AF: 0.648 AC: 2256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.77
DANN	Benign	0.66
PhyloP100		-0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6560936; hg19: chr13-114945972;